If you want to use a sequence of Terminal commands, you can put them in a shell script file (e.g., file /Users/myname/myscript), give the file execute permission (with the command chmod ugo+x /Users/myname/myscript), and then have AppleScript invoke the script rather than invoking a single Terminal command.
--- Example ---
Applescript:
tell application "Terminal" to do script "/Users/myname/myscript"
File /Users/myname/myscript:
#! /bin/sh
cd /Users/myname/perlstuff
...perl conversion command...
...other commands...